Magashule, who was speaking at the ANC’s cadres assembly in Parys, said it made sense for those MPs to willingly resign.
Zuma survived a motion of no confidence in his presidency, held via secret ballot in Parliament on Tuesday.
Following a two-hour debate 198 MPs voted against the Democratic Alliance's bid to remove Zuma, while 177 voted for Zuma to go.
About 30 ANC MPs voted for Zuma to be removed.
A simple majority of 201 votes was required to unseat Zuma as president. Magashule said the MPs who had disobeyed party instructions were now forcing the ANC to kick them out.
He also accused some in the party's national structure of working with the EFF and the DA. He claimed that he had proof of his allegations and that he would reveal this in the future.
"We have ample evidence [that] some are actually working with the DA, I’m just talking nationally, to dislodge the ANC out of power." He appealed to those MPs who had voted against the party to come "to their senses, focus and never sell out the revolution".
The party is currently having its cadre’s assembly, instead, to iron out its internal issues. Zuma, as well as presidential hopeful Nkosazana Dlamini-Zuma, are expected to attend the assembly.
"We postponed the conference to give any other member who is not happy to raise his or her concern. So that, when we go to conference, we are happy that everybody is covered. We want every single individual that is either aggrieved by us or by the ANC to come back and make sure that we work together and we rebuild and refocus..." he said.
'Manyoni is still my friend'
Manyoni, who was once Magashule’s close ally, recently resigned as a Member of Parliament, setting his sights on taking over from Magashule.
Things turned sour between the two men when Magashule fired Manyoni as Mangaung mayor. Magashule, however, denied claims that the two were at odds, saying that he was still good friends with Manyoni.
"Manyoni is still my friend. We are still in good books. At the right time, you will see we are still very good friends."
He, however, could not explain why Manyoni was absent.
Following the election of Cyril Ramaphosa as the ANC president, many people are calling for Jacob Zuma to be sacked as the country's president. What's your take on this?